Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

The application of microwave radiation to analytical and environment chemistry

This review presents the latest advances in the application of microwave energy to analytical chemistry. The fundamental principles of microwave field interaction with the matter are presented and their significance for the chemist is discussed, followed by the basic principles of microwave equipment construction and operation. Examples of the techniques that utilized microwave energy for digestion, extraction, chemical reaction, preconcentration, and desorption of the analytical sample are presented. A separate section describes the examples of usage of microwave technology in catalysis, environmental, and nuclear chemistry and engineering.

Stress transfer and damage evolution simulations of fiber-reinforced polymer-matrix composites

The stress transfer from broken fibers to unbroken fibers in fiber-reinforced thermosetting polymer-matrix composites and thermoplastic polymer-matrix composites was studied using a detailed finite element model. In order to check the validity of this approach, an epoxy-matrix monolayer composite was used as thermosetting polymer-matrix composite and a polypropylene (PP)-matrix monolayer composite was used as thermoplastic polymer-matrix composite, respectively. It is found that the stress concentrations near the broken fiber element cause damage to the neighboring epoxy matrix prior to the breakage of other fibers, whereas in the case of PP-matrix composites the fibers nearest to the broken fiber break prior to the PP matrix damage, because the PP matrix around the broken fiber element yields. In order to simulate composite damage evolution, a Monte Carlo technique based on a finite element method has been developed in the paper. The finite element code coupled with statistical model of fiber strength specifically written for this problem was used to determine the stress redistribution. Five hundred samples of numerical simulation were carried out to obtain statistical deformation and failure process of composites with fixed fiber volume fraction.

泥河湾盆地大长梁剖面岩石磁学和环境磁学研究

The fluvio-lacustrine sequence in the Nihewan Basin is an important archive of late Pliocene-Pleistocene climate and environment changes in temperate northern China, which provides excellent sources of early human settlements in high latitude East Asia. The recent years have witnessed a considerable progress in the paleomagnetic dating of its stratigraphy, which has notably increased our understanding of a series of important issues such as the early human occupation in the Old World, the infilling history of the Nihewan Basin, and the chronological sequence of the Nihewan faunas. Up to now, the long-term paleoenvironmental changes directly retrieved from this basin, which might influence the evolution and expansion of early humans in the Nihewan Basin, are still poorly constrained, although several paleoclimatic records have been retrieved from this area. In this study, a combined mineral-magnetic and geochemical investigation was carried out on the fluvio-lacustrine sequence from the Dachangliang section at the eastern margin of the basin in order to reveal its rock magnetic and environmental magnetic characteristics and its implications for early human evolution in East Asia. The major findings and conclusions are listed as the following: First, there is an increased cooling coupled with an intensified aridification recorded in the fluvio-lacustrine sequence of the Dachangliang section. The cooling is related to an up-section decrease in propensity to chemical weathering as inferred from an increase in low-field susceptibility after cycling to 700 °C. Close to 700 °C, reacting chlorite is providing the iron source for newly formed very fine-grained ferrimagnetic minerals which enhances the susceptibility signal. The reactivity of chlorite after annealing at temperatures above 600 °C is documented with X-ray diffraction. Second, degrees of chemical weathering in the Nihewan Basin are further estimated by clay mineralogy (i.e. chlorite and illite contents and chlorite/illite ratio) and a series of major element proxies (i.e. Na2O/Al2O3 versus K2O/Al2O3 diagram, Al2O3-(CaO + Na2O)-K2O ternary diagram (A-CN-K), chemical index of alteration (CIA), (CaO + Na2O + MgO)/TiO2, (CaO + Na2O + MgO + K2O)/(TiO2 + Al2O3), CaO/Al2O3 and CaO/TiO2). The up-section decrease in propensity to chemical weathering suggested by the aforementioned rock mangetic measurement is further confirmed by these geochemical analyses. Combining the chemical weathering records from the Nihewan Basin, Chinese Loess Plateau, South China Sea and eastern China, we find that the consecutive decreasing trend in chemical weathering intensity during the late Cenozoic is ubiquitous across China. This pattern may result from a long-term decreasing East Asian summer monsoon and increasing East Asian winter monsoon, and thus a consecutive increasing of aridification and cooling in Asia during the Quaternary. Furthermore, the chemical weathering intensity increased from South China to North China during the Quaternary, in line with the decreasing East Asian summer monsoon and increasing East Asian winter monsoon and thus the gradually intensified aridification and cooling from South China to North China. Third, a combined mineral-magnetic and geochemical investigation provides evidences that the large-amplitude alterations of concentration of magnetic minerals mainly result from preservation/dissolution cycles of detrital magnetic minerals in alternately oxic and anoxic depositional environments. The preservation/dissolution model implies that the high-magnetic and low-magnetic cycles of this sedimentary sequence represent glacial and interglacial climate cycles, respectively. This contribute significnatly to our understanding of the link between climate and magnetic properties. Finally, the paleoclimatic implications of these rock magnetic and geochemical characteristics significantly increase our understanding of the general setting of early humans in high northern latitude in East Asia. We propose that the cold and dry climate may have contributed significantly to the expansion and adaptation of early humans, rather than bringing hardship, as is often thought. The relationship between magnetic properties and climate possibly provides valuable information on the climatic context of the Paleolithic sites in the basin, especially whether the occupation occurred during an interglacial or glacial period.

The role of tectonic uplift, climate, and vegetation in the long-term terrestrial phosphorous cycle

Phosphorus (P) is a crucial element for life and therefore for maintaining ecosystem productivity. Its local availability to the terrestrial biosphere results from the interaction between climate, tectonic uplift, atmospheric transport, and biotic cycling. Here we present a mathematical model that describes the terrestrial P-cycle in a simple but comprehensive way. The resulting dynamical system can be solved analytically for steady-state conditions, allowing us to test the sensitivity of the P-availability to the key parameters and processes. Given constant inputs, we find that humid ecosystems exhibit lower P availability due to higher runoff and losses, and that tectonic uplift is a fundamental constraint. In particular, we find that in humid ecosystems the biotic cycling seem essential to maintain long-term P-availability. The time-dependent P dynamics for the Franz Josef and Hawaii chronosequences show how tectonic uplift is an important constraint on ecosystem productivity, while hydroclimatic conditions control the P-losses and speed towards steady-state. The model also helps describe how, with limited uplift and atmospheric input, as in the case of the Amazon Basin, ecosystems must rely on mechanisms that enhance P-availability and retention. Our novel model has a limited number of parameters and can be easily integrated into global climate models to provide a representation of the response of the terrestrial biosphere to global change. © 2010 Author(s).

Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

Cellular stresses activate the tumor suppressor p53 protein leading to selective binding to DNA response elements (REs) and gene transactivation from a large pool of potential p53 REs (p53REs). To elucidate how p53RE sequences and local chromatin context interact to affect p53 binding and gene transactivation, we mapped genome-wide binding localizations of p53 and H3K4me3 in untreated and doxorubicin (DXR)-treated human lymphoblastoid cells. We examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 hypersensitivity, DHS), ENCODE chromatin states, p53RE sequence, and evolutionary conservation. We observed that the inducible expression of p53-regulated genes was associated with the steady-state chromatin status of the cell. Most highly inducible p53-regulated genes were suppressed at baseline and marked by repressive histone modifications or displayed CTCF binding. Comparison of p53RE sequences residing in different chromatin contexts demonstrated that weaker p53REs resided in open promoters, while stronger p53REs were located within enhancers and repressed chromatin. p53 occupancy was strongly correlated with similarity of the target DNA sequences to the p53RE consensus, but surprisingly, inversely correlated with pre-existing nucleosome accessibility (DHS) and evolutionary conservation at the p53RE. Occupancy by p53 of REs that overlapped transposable element (TE) repeats was significantly higher (p<10-7) and correlated with stronger p53RE sequences (p<10-110) relative to nonTE-associated p53REs, particularly for MLT1H, LTR10B, and Mer61 TEs. However, binding at these elements was generally not associated with transactivation of adjacent genes. Occupied p53REs located in L2-like TEs were unique in displaying highly negative PhyloP scores (predicted fast-evolving) and being associated with altered H3K4me3 and DHS levels. These results underscore the systematic interaction between chromatin status and p53RE context in the induced transactivation response. This p53 regulated response appears to have been tuned via evolutionary processes that may have led to repression and/or utilization of p53REs originating from primate-specific transposon elements.

Continuous Plankton Records - Phytoplankton Zooplankton And Environment Northeast Atlantic And North-Sea 1958-1980

Year-to-year fluctuations in the abundance of phytoplankton in the North-East Atlantic and the North Sea for the period 1958 to 1980 are described. Based on similarities between their annual fluctuations in abundance, the taxa may be divided into two groups, one of 12 species of diatoms and 1 species of Ceratium, the other of 5 species of Ceratium. The annual fluctuations in abundance of the Ceratium group is negatively correlated with a component of sea surface temperature (representing changes in the open ocean) and with the frequency of cyclonic weather over the United Kingdom. The Diatom group shows very similar annual fluctuations to those of most of the zooplankton species. Both groups show a high ·proportion of long wavelength variability in the form of a more less linear downward trend in abundance over the whole period. There is evidence to suggest that the high proportion of long wavelength variability shown by the zooplankton is influenced by inherent persistence in stocks from year-to year. The phytoplankton show little or no persistence. The close relationship between zooplankton and phytoplankton may, therefore, involve feed-back through nutrient recycling so influencing the annual levels of abundance of phytoplankton.

Decadal changes in climate and ecosystems in the North Atlantic Ocean and adjacent seas

Climate change is unambiguous and its effects are clearly detected in all functional units of the Earth system. This study presents new analyses of sea-surface temperature changes and show that climate change is affecting ecosystems of the North Atlantic. Changes are seen from phytoplankton to zooplankton to fish and are modifying the dominance of species and the structure, the diversity and the functioning of marine ecosystems. Changes also range from phenological to biogeographical shifts and have involved in some regions of the Atlantic abrupt ecosystem shifts. These alterations reflect a response of pelagic ecosystems to a warmer temperature regime. Mechanisms are complex because they are nonlinear exhibiting tipping points and varying in space and time. Sensitivity of organisms to temperature changes is high, implicating that a small temperature modification can have sustained ecosystem effects. Implications of these changes for biogeochemical cycles are discussed. Two observed changes detected in the North Sea that could have opposite effects on carbon cycle are discussed. Increase in phytoplankton, as inferred from the phytoplankton colour index derived from the Continuous Plankton Recorder (CPR) survey, has been detected in the North Sea. This pattern has been accompanied by a reduction in the abundance of the herbivorous species Calanus finmarchicus. This might have reduced the grazing pressure and increase diatomaceous ‘fluff’, therefore carbon export in the North Sea. Therefore, it could be argued that the biological carbon pump might increase in this region with sea warming. In the meantime, however, the mean size of organisms (calanoid copepods) has dropped. Such changes have implications for the turnover time of biogenic carbon in plankton organisms and the mean residence time of particulate carbon they produce. The system characterising the warmer period is more based on recycling and less on export. The increase in the minimum turnover time indicates an increase in the ecosystem metabolism, which can be considered as a response of the pelagic ecosystems to climate warming. This phenomenon could reduce carbon export. These two opposite patterns of change are examples of the diversity of mechanisms and pathways the ecosystems may exhibit with climate change. Oversimplification of current biogeochemical models, often due to lack of data and biological understanding, could lead to wrong projection on the direction ecosystems and therefore some biogeochemical cycles might take in a warmer world.